tbuckley/cabot-search huggingface dataset:
Evolution is not Uniform Along Coding Sequences
Authors: Raphaël Bricout, Dominique Weil, David Stroebel, Auguste Genovesio, Hugues Roest Crollius
Journal: Molecular Biology and Evolution (2023)

Abstract Amino acids evolve at different speeds within protein sequences, because their functional and structural roles are different. Notably, amino acids located at the surface of proteins are known to evolve more rapidly than those in the core. In particular, amino acids at the N- and C-termini of protein sequences are likely to be more exposed than those at the core of the folded protein due to their location in the peptidic chain, and they are known to be less structured. Because of these reasons, we would expect that amino acids located at protein termini would evolve faster than residues located inside the chain. Here we test this hypothesis and found that amino acids evolve almost twice as fast at protein termini compared with those in the center, hinting at a strong topological bias along the sequence length. We further show that the distribution of solvent-accessible residues and functional domains in proteins readily explain how structural and functional constraints are weaker at their termini, leading to the observed excess of amino acid substitutions. Finally, we show that the specific evolutionary rates at protein termini may have direct consequences, notably misleading in silico methods used to infer sites under positive selection within genes. These results suggest that accounting for positional information should improve evolutionary models.
Strategies to Improve Adherence to Skin Self-examination and Other Self-management Practices in People at High Risk of Melanoma
Authors: Deonna M. Ackermann, Karen Bracken, Monika Janda, Robin M. Turner, Jolyn K. Hersch, Dorothy Drabarek, Katy J. L. Bell
Journal: JAMA Dermatology (2023)

Importance Adherence, both in research trials and in clinical practice, is crucial to the success of interventions. There is limited guidance on strategies to increase adherence and the measurement and reporting of adherence in trials of melanoma self-management practices. Objective This scoping review aimed to describe (1) strategies to improve adherence to self-management practices in randomized clinical trials of people at high risk of melanoma and (2) measurement and reporting of adherence data in these trials. Evidence Review Four databases, including MEDLINE, Embase, CENTRAL, and CINAHL, were searched from inception to July 2022. Eligible studies were randomized clinical trials of self-monitoring interventions for early detection of melanoma in people at increased risk due to personal history (eg, melanoma, transplant, dysplastic naevus syndrome), family history of melanoma, or as determined by a risk assessment tool or clinical judgment. Findings From 939 records screened, 18 eligible randomized clinical trials were identified, ranging in size from 40 to 724 participants, using a range of adherence strategies but with sparse evidence on effectiveness of the strategies. Strategies were classified as trial design (n = 15); social and economic support (n = 5); intervention design (n = 18); intervention and condition support (n = 10); and participant support (n = 18). No strategies were reported for supporting underserved groups (eg, people who are socioeconomically disadvantaged, have low health literacy, non-English speakers, or older adults) to adhere to self-monitoring practices, and few trials targeted provider (referring to both clinicians and researchers) adherence (n = 5). Behavioral support tools included reminders (n = 8), priority-setting guidance (n = 5), and clinician feedback (n = 5). Measurement of adherence was usually by participant report of skin self-examination practice with some recent trials of digital interventions also directly measuring adherence to the intervention through website or application analytic data. Reporting of adherence data was limited, and fewer than half of all reports mentioned adherence in their discussion. Conclusions and Relevance Using an adaptation of the World Health Organization framework for clinical adherence, this scoping review of randomized clinical trials identified key concepts as well as gaps in the way adherence is approached in design, conduct, and reporting of trials for skin self-examination and other self-management practices in people at high risk of melanoma. These findings may usefully guide future trials and clinical practice; evaluation of adherence strategies may be possible using a Study Within A Trial (SWAT) framework within host trials.
A Young Woman With Dyspnea During Cardiac Catheterization
Authors: Praveen Gupta
Journal: JAMA Cardiology (2023)

A woman in her mid-20s was evaluated for a history of dyspnea on exertion for 2 years. A 6F pigtail catheter was placed in the left ventricle via the right femoral artery, but the patient developed acute onset of dyspnea along with retrosternal chest pain; the catheter was pulled back into the right atrium, and chest fluoroscopy was performed. What would you do next?
A Rocky Resurgence
Authors: John W. Ostrominski, Thomas E. Clancy, Lynn Bry, Bruce D. Levy, Joseph Loscalzo
Journal: New England Journal of Medicine (2023)

A 70-year-old woman presented with 2 months of progressive abdominal pain in the right upper quadrant. She also reported intermittent fevers, sweating, nausea, anorexia, fatigue, and unintentional weight loss.
Critical Appraisal of the Negative Predictive Performance of the European Society of Cardiology 0/1-Hour Algorithm for Evaluating Patients With Chest Pain in the US
Authors: Júlia Karády, David A. Morrow
Journal: JAMA Cardiology (2023)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Cardiology HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Cardiology journal
Evaluation of the clinical significance of global <scp>mRNA</scp> alternative splicing in patients with acute myeloid leukemia
Authors: Yi‐Tsung Yang, Chi‐Yuan Yao, Po‐Ju Chiu, Chein‐Jun Kao, Hsin‐An Hou, Chien‐Chin Lin, Wen‐Chien Chou, Hwei‐Fang Tien
Journal: American Journal of Hematology (2023)

Abstract Aberrant alternative splicing (AS) is involved in leukemogenesis. This study explored the clinical impact of alterations in global AS patterns in 341 patients with acute myeloid leukemia (AML) newly diagnosed at the National Taiwan University Hospital and validated it using The Cancer Genome Atlas (TCGA) cohort. While studying normal cord blood CD34 + /CD38 − cells, we found that AML cells exhibited significantly different global splicing patterns. AML with mutated TP53 had a particularly high degree of genome‐wide aberrations in the splicing patterns. Aberrance in the global splicing pattern was an independent unfavorable prognostic factor affecting the overall survival of patients with AML receiving standard intensive chemotherapy. The integration of global splicing patterns into the 2022 European LeukemiaNet risk classification could stratify AML patients into four groups with distinct prognoses in both our experimental and TCGA cohorts. We further identified four genes with AS alterations that harbored prognostic significance in both of these cohorts. Moreover, these survival‐associated AS events are involved in several important cellular processes that might be associated with poor response to intensive chemotherapy. In summary, our study demonstrated the clinical and biological implications of differential global splicing patterns in AML patients. Further studies with larger prospective cohorts are required to confirm these findings.
Early-Onset Colorectal Cancer Somatic Gene Mutations by Population Subgroups
Authors: Xinyi Shen, Andrew T. DeWan, Caroline H. Johnson
Journal: Cancer Discovery (2023)

In this issue of Cancer Discovery, Holowatyj and colleagues uncover racial/ethnic and sex heterogeneity in somatic mutations among patients with early-onset colorectal cancer. The findings shed light on a deeper understanding of complex biological and genetic mechanisms for colorectal cancer in diverse populations. See related article by Holowatyj et al., p. 570 (6).
Neutralization of BQ.1, BQ.1.1, and XBB with RBD-Dimer Vaccines
Authors: Dedong Li, Minrun Duan, Xiao Wang, Pengyue Gao, Xin Zhao, Kun Xu, George F Gao
Journal: New England Journal of Medicine (2023)

n d e n c e Neutralization of BQ.1, BQ.1.1,and XBB with RBD-Dimer Vaccines To the Editor: Several B.1.1.529(omicron) subvariants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging and have become the dominant strains, such as BF.7, BQ.1, BQ.1.1,and XBB.These variants contain more mutations in the spike protein receptorbinding domain (RBD) than the BA.2 and BA.5 strains (Fig. 1A).Therefore, the potential of these omicron subvariants for immune evasion is a concern.The coronavirus disease 2019 (Covid-19) vaccines with inactivated virus (CoronaVac and BBIBP-CorV) and the ZF2001 protein subunit vaccine 1 have been widely used in China and many other countries.In this study, we obtained serum samples from vaccinees (age range, 18 to 59 years) who had received three homologous doses of ZF2001 (the ZF2001 group, 16 participants) or inactivated vaccine (the inactivatedvaccine group, 16 participants) or two doses of inactivated vaccine plus a booster dose of ZF2001 (the heterologous-boost group, 16 participants) (Fig. S1 in the Supplementary Appendix, available with the full text of this letter at NEJM.org).this week's letters Neutralization of BQ.1, BQ.1.1,and XBB with RBD-Dimer Vaccines Once-Weekly Semaglutide in Adolescents with Obesity Efficacy and Safety of Bepirovirsen in Hepatitis B New Approaches to Chronic Hepatitis B Focused Cardiac Ultrasonography for Right Ventricular Size and Systolic Function Bivalent Covid-19 Vaccines Figure 1 (facing page).Vaccine-Elicited Neutralizing Antibodies against SARS-CoV-2 Variants in Human and Murine Serum Samples.
Pharmacotherapies for Treatment-Resistant Depression: How Antipsychotics Fit in the Rapidly Evolving Therapeutic Landscape
Authors: Manish K. Jha, Sanjay J. Mathew
Journal: American Journal of Psychiatry (2023)

One in three adults with major depressive disorder (MDD) do not experience clinically significant improvement after multiple sequential courses of antidepressants and have treatment-resistant depression (TRD). The presence of TRD contributes to the morbidity and excess mortality associated with MDD and has been linked to significantly increased health care expenses. In the absence of a consensus definition of TRD, this report takes a broad approach by considering inadequate response to one or more courses of antidepressants and focuses on atypical antipsychotics that are approved by the U.S. Food and Drug Administration for treatment of depression (aripiprazole, brexpiprazole, cariprazine, extended-release quetiapine, and olanzapine-fluoxetine combination). While multiple acute-phase studies have demonstrated the efficacy of these medications in improving depressive symptoms, clinically meaningful improvement (i.e., remission) remains limited, with significant concerns about side effects (including weight gain, metabolic dysfunction, extrapyramidal symptoms, and tardive dyskinesia), especially with long-term use. With the rapidly evolving landscape of antidepressant treatments over the past few years, which has witnessed approval of rapid-acting antidepressants (e.g., esketamine nasal spray and dextromethorphan-bupropion combination) and several more in the late-stage pipeline (e.g., zuranolone and psilocybin), it remains to be seen whether the use of atypical antipsychotics will go the way of the older and rarely prescribed antidepressants (such as tricyclics and monoamine oxidase inhibitors). Pragmatic clinical trials are needed to compare the effectiveness of atypical antipsychotics with TRD-specific pharmacotherapies and neuromodulation treatments and to identify the optimal sequencing of these varied approaches for patients with MDD. When using atypical antipsychotics, clinicians and patients are encouraged to use a shared decision-making approach by personalizing treatment selection based on anticipated side effects, tolerability, cost, and feasibility.
Time to Surgery in Breast Cancer—Is Faster Always Better?
Authors: Rita A. Mukhtar, Laura J. Esserman
Journal: JAMA Surgery (2023)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Surgery HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Surgery journal
Health data justice: building new norms for health data governance
Authors: James Shaw, Sharifah Sekalala
Journal: npj Digital Medicine (2023)

Abstract The retention and use of health-related data by government, corporate, and health professional actors risk exacerbating the harms of colonial systems of inequality in which health care and public health are situated, regardless of the intentions about how those data are used. In this context, a data justice perspective presents opportunities to develop new norms of health-related data governance that hold health justice as the primary objective. In this perspective, we define the concept of health data justice, outline urgent issues informed by this approach, and propose five calls to action from a health data justice perspective.
Meta-analysis: COVID-19 Infection Protects Against Severe Disease
Authors: Emily Harris
Journal: JAMA (2023)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Financial Impact of Metabolic Surgery on Prescription Diabetes Medications in Michigan
Authors: Oliver A. Varban, Kristen P. Hassett, Monica Yost, Arthur M. Carlin, Amir A. Ghaferi, Jonathan F. Finks, Anne P. Ehlers
Journal: JAMA Surgery (2023)

This study compares expenditures for diabetes medications before and after metabolic surgery among patients with diabetes in Michigan.
Operative Outcomes of Women Undergoing Coronary Artery Bypass Surgery in the US, 2011 to 2020
Authors: Mario Gaudino, David Chadow, Mohamed Rahouma, Giovanni Jr Soletti, Sigrid Sandner, Roberto Perezgrovas-Olaria, Katia Audisio, Gianmarco Cancelli, Brenden A. Bratton, Stephen Fremes, Paul Kurlansky, Leonard Girardi, Robert H. Habib
Journal: JAMA Surgery (2023)

Importance It has been reported that women undergoing coronary artery bypass have higher mortality and morbidity compared with men but it is unclear if the difference has decreased over the last decade. Objective To evaluate trends in outcomes of women undergoing coronary artery bypass in the US from 2011 to 2020. Design, Setting, and Participants This retrospective cohort study at hospitals contributing to the Adult Cardiac Surgery Database of the Society of Thoracic Surgeons included 1 297 204 patients who underwent primary isolated coronary artery bypass from 2011 to 2020. Exposure Coronary artery bypass. Main Outcomes and Measures The primary outcome was operative mortality. The secondary outcome was the composite of operative mortality and morbidity (including operative mortality, stroke, kidney failure, reoperation, deep sternal wound infection, prolonged mechanical ventilation, and prolonged hospital stay). The attributable risk (the association of female sex with coronary artery bypass grafting outcomes) for the primary and secondary outcomes was calculated. Results Between 2011 and 2020, 1 297 204 patients underwent primary isolated coronary artery bypass grafting with a mean age of 66.0 years, 317 716 of which were women (24.5%). Women had a higher unadjusted operative mortality (2.8%; 95% CI, 2.8-2.9 vs 1.7%; 95% CI, 1.7-1.7; P &amp;amp;lt; .001) and overall unadjusted incidence of the composite of operative mortality and morbidity compared with men (22.9%; 95% CI, 22.7-23.0 vs 16.7%; 95% CI, 16.6-16.8; P &amp;amp;lt; .001). The attributable risk of female sex for operative mortality varied from 1.28 in 2011 to 1.41 in 2020, with no significant change over the study period ( P for trend = 0.38). The attributable risk for the composite of operative mortality and morbidity was 1.08 in both 2011 and 2020 with no significant change over the study period ( P for trend = 0.71). Conclusions and Relevance Women remain at significantly higher risk for adverse outcomes following coronary artery bypass grafting and no significant improvement has been seen over the course of the last decade. Further investigation into the determinants of operative outcomes in women is urgently needed.
Trends in Supply of Nursing Home Beds, 2011-2019
Authors: Katherine E. M. Miller, Paula Chatterjee, Rachel M. Werner
Journal: JAMA Network Open (2023)

Importance Nursing homes play a vital role in providing postacute and long-term care for individuals whose needs cannot be met in the home or community. Whether the supply of nursing home beds and, specifically, the supply of high-quality beds has kept pace with the growth of the older adult population is unknown. Objective To describe changes in the supply of population-adjusted nursing home beds from 2011 to 2019. Design, Setting, and Participants This cross-sectional study examines changes in the population-adjusted supply of nursing home beds across all US counties from 2011 to 2019 and describes county and nursing home characteristics where the supply of nursing home beds has increased vs decreased. Main Outcomes and Measures Number of nursing home beds adjusted per 10 000 adults aged 65 years and older. Results The population-adjusted supply of nursing home beds declined from 2011 to 2019 for 86.4% of US counties, by a mean (SD) of 129.9 (123.8) beds per 10 000 adults aged 65 years or older per county from a baseline mean (SD) of 552.5 (274.4) beds per 10 000 adults aged 65 years or older per county in 2011. The share of beds that were high quality (4- or 5-star ratings) also declined, which was driven by a small number of counties where nursing home bed supply increased due to a proliferation of lower-quality beds. Simultaneously, metropolitan counties with declining numbers of nursing home beds also experienced declining number of senior housing residential beds (−11.3 [54.6] beds per 10 000 adults aged 65 years or older per county from a baseline mean [SD] of 354.8 [222.3]). Conclusions and Relevance The findings of this cross-sectional study suggest that the supply of nursing home beds, specifically high-quality nursing home beds, and senior residential housing beds have not kept pace with the demographics of an aging population. Understanding the supply of high-quality nursing home beds and associated geographic variation can inform targeted policies to best support older adults requiring nursing home care.
Functional and Safety Outcomes of Carotid Artery Stenting and Mechanical Thrombectomy for Large Vessel Occlusion Ischemic Stroke With Tandem Lesions
Authors: Mudassir Farooqui, Osama O. Zaidat, Ameer E. Hassan, Darko Quispe-Orozco, Nils Petersen, Afshin A. Divani, Marc Ribo, Michael Abraham, Johanna Fifi, Waldo R. Guerrero, Amer M. Malik, James E. Siegler, Thanh N. Nguyen, Sunil Sheth, Albert J. Yoo, Guillermo Linares, Nazli Janjua, Milagros Galecio-Castillo, Wondewossen G. Tekle, Victor M. Ringheanu, Marion Oliver, Giana Dawod, Jessica Kobsa, Ayush Prasad, Asad Ikram, Eugene Lin, Kristine Below, Cynthia B. Zevallos, Marta Olivé Gadea, Abid Qureshi, Andres Dajles, Stavros Matsoukas, Ameena Rana, Mohamad Abdalkader, Sergio Salazar-Marioni, Jazba Soomro, Weston Gordon, Juan Vivanco-Suarez, Charoskhon Turabova, Maxim Mokin, Dileep R. Yavagal, Mouhammad A. Jumaa, Santiago Ortega-Gutierrez
Journal: JAMA Network Open (2023)

Approximately 10% to 20% of large vessel occlusion (LVO) strokes involve tandem lesions (TLs), defined as concomitant intracranial LVO and stenosis or occlusion of the cervical internal carotid artery. Mechanical thrombectomy (MT) may benefit patients with TLs; however, optimal management and procedural strategy of the cervical lesion remain unclear.